6 Milo: differential abundance

sclet provides a lightweight wrapper around miloR for cell neighbourhood differential abundance (DA) analysis. The Milo functionality in sclet is an optional dependency: you need to install miloR to run the examples.

6.1 Requirements

Before running Milo DA, prepare a SingleCellExperiment with:

reducedDims(sce)$PCA
colData(sce) containing a sample column and a condition column

UMAP is optional (used for visualization only).

6.2 Two-group DA (GLM)

library(MouseThymusAgeing)
library(scater)

sce <- MouseSMARTseqData()

## see ?MouseThymusAgeing and browseVignettes('MouseThymusAgeing') for documentation

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colData(sce)$Sample <- paste(colData(sce)$SortDay, colData(sce)$Age, sep = "_")

sce <- logNormCounts(sce)

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sce <- runPCA(sce)

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sce <- runUMAP(sce)

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res <- runMilo(
  sce = sce,
  sample_col = "Sample",
  condition_col = "Age",
  contrasts = c("Age1wk - Age4wk"),
  k1 = 11, k2 = 11, d1 = 40, d2 = 40, prop = 0.2
)

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## Constructing kNN graph with k:11

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## Checking valid object

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## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## 'as(<dgTMatrix>, "dgCMatrix")' is deprecated.
## Use 'as(., "CsparseMatrix")' instead.
## See help("Deprecated") and help("Matrix-deprecated").

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running with model contrasts

## Performing spatial FDR correction with graph-overlap weighting

da <- res$da_results
table(da$SpatialFDR < 0.1)

## 
## FALSE  TRUE 
##   293    33

head(da)

##        logFC   logCPM          F       PValue         FDR
## 1 -0.4041183 13.89024  0.1969714 6.571914e-01 0.886248883
## 2 -1.7429777 13.44896  1.9856283 1.588464e-01 0.395297203
## 3 -2.5426138 13.43925  3.6630508 5.567541e-02 0.235716683
## 4 -1.2096484 13.72997  1.2479469 2.639861e-01 0.541956321
## 5 -5.1188767 14.09717 15.5551317 8.097396e-05 0.006656048
## 6 -2.1080557 13.68153  2.9605848 8.536452e-02 0.288426813
##   Nhood  SpatialFDR        contrast PValue_adj_withinNhood
## 1     1 0.922512043 Age1wk - Age4wk           6.571914e-01
## 2     2 0.394819240 Age1wk - Age4wk           1.588464e-01
## 3     3 0.247678269 Age1wk - Age4wk           5.567541e-02
## 4     4 0.543297667 Age1wk - Age4wk           2.639861e-01
## 5     5 0.007590456 Age1wk - Age4wk           8.097396e-05
## 6     6 0.289038829 Age1wk - Age4wk           8.536452e-02

6.3 Multi-contrast testing

Use per_contrast = FALSE to fit one model and test multiple contrasts jointly. Use per_contrast = TRUE to run each contrast and stack results.

contrasts <- c(
  "Age1wk - Age4wk",
  "Age4wk - Age16wk",
  "Age16wk - Age32wk",
  "Age32wk - Age52wk"
)

res2 <- runMilo(
  sce = sce,
  sample_col = "Sample",
  condition_col = "Age",
  contrasts = contrasts,
  per_contrast = TRUE,
  k1 = 11, k2 = 11, d1 = 40, d2 = 40, d3 = 40,
  prop = 0.2,
  refinement_scheme = "graph"
)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Constructing kNN graph with k:11

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Checking valid object

## Running refined sampling with graph

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Checking meta.data validity

## Counting cells in neighbourhoods

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running with model contrasts

## Performing spatial FDR correction with graph-overlap weighting

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running with model contrasts

## Performing spatial FDR correction with graph-overlap weighting

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running with model contrasts

## Performing spatial FDR correction with graph-overlap weighting

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running with model contrasts

## Performing spatial FDR correction with graph-overlap weighting

head(res2$da_results)

##        logFC   logCPM          F       PValue         FDR
## 1 -0.4041183 13.89024  0.1969714 6.571914e-01 0.886248883
## 2 -1.7429777 13.44896  1.9856283 1.588464e-01 0.395297203
## 3 -2.5426138 13.43925  3.6630508 5.567541e-02 0.235716683
## 4 -1.2096484 13.72997  1.2479469 2.639861e-01 0.541956321
## 5 -5.1188767 14.09717 15.5551317 8.097396e-05 0.006656048
## 6 -2.1080557 13.68153  2.9605848 8.536452e-02 0.288426813
##   Nhood  SpatialFDR        contrast PValue_adj_withinNhood
## 1     1 0.922512043 Age1wk - Age4wk           0.9606996372
## 2     2 0.394819240 Age1wk - Age4wk           0.4475589446
## 3     3 0.247678269 Age1wk - Age4wk           0.1113508256
## 4     4 0.543297667 Age1wk - Age4wk           0.9020010685
## 5     5 0.007590456 Age1wk - Age4wk           0.0003238958
## 6     6 0.289038829 Age1wk - Age4wk           0.3414580859

6.4 GLMM (random intercept)

When samples are not independent (e.g., repeated measures), a random intercept can help control correlation structure.

library(scRNAseq)
library(scater)
library(scran)
library(scuttle)

sce2 <- KotliarovPBMCData(mode = "rna", ensembl = FALSE)

## see ?scRNAseq and browseVignettes('scRNAseq') for documentation

## downloading 1 resources

## retrieving 1 resource

## loading from cache

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## see ?scRNAseq and browseVignettes('scRNAseq') for documentation

## downloading 1 resources

## retrieving 1 resource

## loading from cache

colData(sce2)$ObsID <- paste(colData(sce2)$tenx_lane, colData(sce2)$sampleid, sep = "_")

set.seed(42)
keep_samps <- sample(unique(colData(sce2)$ObsID), size = 40)
sce2 <- sce2[, colData(sce2)$ObsID %in% keep_samps]

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

sce2 <- logNormCounts(sce2)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

sce2 <- runPCA(sce2, ncomponents = 30)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'

sce2 <- runUMAP(sce2, pca = 30)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'

res3 <- runMilo(
  sce = sce2,
  sample_col = "ObsID",
  condition_col = "adjmfc.time",
  contrasts = c("adjmfc.timed0 high"),
  glmm = TRUE,
  random_effect = "tenx_lane",
  k1 = 60, k2 = 60, d1 = 30, d2 = 30, d3 = 30,
  prop = 0.05,
  overlap = 25
)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Constructing kNN graph with k:60

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Checking valid object

## Running refined sampling with graph

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Checking meta.data validity

## Counting cells in neighbourhoods

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Random effects found

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running GLMM model - this may take a few minutes

## Performing spatial FDR correction with graph-overlap weighting

head(res3$da_results)

##        logFC   logCPM        SE     tvalue      PValue
## 1  0.7934436 11.12215 0.3416483  2.3223987 0.020246243
## 2 -0.1708452 11.22119 0.3456940 -0.4942091 0.621175906
## 3 -0.3782762 11.24442 0.3596173 -1.0518855 0.292895276
## 4 -0.1358645 11.20480 0.3809763 -0.3566218 0.721375412
## 5 -1.3891470 11.38580 0.4296563 -3.2331585 0.001224296
## 6 -0.1023156 10.70056 0.3342103 -0.3061413 0.759506728
##   tenx_lane_variance Converged Logliklihood Nhood
## 1         0.00000001      TRUE     273.4813     1
## 2         0.00000001      TRUE     363.1577     2
## 3         0.00000001      TRUE     416.1107     3
## 4         0.69624791     FALSE     473.8265     4
## 5         3.08758363     FALSE     477.9005     5
## 6         0.00000001      TRUE     175.2036     6
##    SpatialFDR           contrast PValue_adj_withinNhood
## 1 0.068207131 adjmfc.timed0 high            0.020246243
## 2 0.722926499 adjmfc.timed0 high            0.621175906
## 3 0.418761745 adjmfc.timed0 high            0.292895276
## 4 0.818637345 adjmfc.timed0 high            0.721375412
## 5 0.008471574 adjmfc.timed0 high            0.001224296
## 6 0.837702119 adjmfc.timed0 high            0.759506728

6.5 Refit after dropping separated neighbourhoods

In GLMM mode, some neighbourhoods can show perfect separation and return unstable estimates. You can diagnose with miloR::checkSeparation() and refit after dropping those neighbourhoods.

design_df <- res3$sce@metadata$milo_results$design_df

bad_hood <- which(miloR::checkSeparation(
  res3$milo,
  design.df = design_df,
  condition = "adjmfc.time",
  min.val = 10
))

refit <- refit_milo(
  milo = res3$milo,
  design_df = design_df,
  bad_hood = bad_hood,
  formula = res3$sce@metadata$milo_results$formula,
  contrasts = res3$sce@metadata$milo_results$contrasts,
  glmm = TRUE,
  old_results = res3$da_results
)

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Random effects found

## Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'

## Also defined by 'alabaster.base'

## Using TMM normalisation

## Running GLMM model - this may take a few minutes

## Performing spatial FDR correction with graph-overlap weighting

## Significant nhoods (FDR<0.1): before=189, after=187

head(refit$da_clean)

##        logFC   logCPM        SE     tvalue       PValue
## 1  0.7934527 11.12215 0.3396978  2.3357604 0.0195376046
## 2 -0.1708541 11.22119 0.3451418 -0.4950259 0.6205992455
## 3 -0.3804964 11.24442 0.3545516 -1.0731763 0.2832360008
## 4 -0.2717697 11.20480 0.3774996 -0.7199204 0.4715785392
## 5 -1.4140809 11.38580 0.4223620 -3.3480303 0.0008138813
## 6 -0.1023156 10.70056 0.3342103 -0.3061413 0.7595067279
##   tenx_lane_variance Converged Logliklihood Nhood
## 1        0.000000010      TRUE     273.4232     1
## 2        0.000000010      TRUE     363.1333     2
## 3        0.001056609     FALSE     421.7318     3
## 4        0.402062578     FALSE     471.1950     4
## 5        2.547672153     FALSE     477.6008     5
## 6        0.000000010      TRUE     175.2036     6
##    SpatialFDR
## 1 0.071527806
## 2 0.729010636
## 3 0.423572700
## 4 0.595822861
## 5 0.008114838
## 6 0.842946543